Number of runs: 17
Number of samples: 4317
Number of controls: 396
India Malawi UK
BM1 334 133 92
BM2 301 97 42
BM3 298 89 41
BS1 354 130 104
BS2 316 86 64
BS3 318 79 58
BS4 0 95 60
BS5 336 104 88
BS6 0 81 61
MS1 337 121 98
run n min med max
1 LIMS12416 53.0 85.0 111203.0 7127326.0
2 LIMS12651 170.0 316.0 177221.5 3919893.0
3 LIMS14462l1 370.0 0.0 86285.5 756928.0
4 LIMS14462l2 364.0 0.0 84133.0 1839299.0
5 LIMS14801 95.0 0.0 73892.0 333405.0
6 LIMS15089 370.0 3.0 110796.5 3748639.0
7 LIMS15168 89.0 32.0 513390.0 1060421.0
8 LIMS15350 323.0 0.0 156639.0 661343.0
9 LIMS15914 348.0 0.0 122788.5 534346.0
10 LIMS15990 356.0 0.0 127734.0 422886.0
11 LIMS16518 357.0 0.0 48510.0 1534696.0
12 LIMS16519 354.0 0.0 87388.5 1945706.0
13 LIMS17407 343.0 0.0 126279.0 921853.0
14 LIMS18668 370.0 0.0 119663.0 1057161.0
15 LIMS18669 367.0 0.0 113045.0 632275.0
16 p1p2 192.0 0.0 58134.0 89725.0
17 p3p4 192.0 0.0 57241.5 90699.0
sample group n min med max
1 breastmilk 1427.0 0.0 88021.0 3748639.0
2 ctrl 396.0 0.0 66137.0 7127326.0
3 infant stool 2334.0 0.0 119591.0 3919893.0
4 maternal stool 556.0 78.0 102317.5 1569457.0
N samples: 2137
[1] "tLIMS12651p1s90WCSctrl" "tLIMS14462l1s277I077toI096WCSctrl"
[3] "tLIMS14462l1s366I058toI076WCSctrl" "tLIMS14462l1s90I038toI056WCSctrl"
[5] "tLIMS18669s150WCSIctrl14" "tLIMS18669s160WCSIctrl27"
Stool samples/controls * n samples: 4302
* n controls: 360
* n features: 10159
Lines display depths of 10,000, 25,000 and 50,000 sequences. Abbreviations: BM, breastmillk; BS, baby stool; MS, maternal stool.
n d10k d25k d50k
BM 1325 1283 1206 1012
BS 2025 1979 1971 1927
MS 446 442 440 429
Rarefaction depth of 2.510^{4} sequences per sample retains 97.3% of infant samples, 98.7% of maternal samples, and 91% of breastmilk samples.
n_samples n_taxa total_count min mean sd
ps1 (unfiltered) 4680 81278 599439742 2 128085 177663
ps2 (length) 4680 69094 596953865 2 127554 177552
ps3 (taxonomy) 4680 66231 595091220 2 127156 177351
ps4 (≥0.1% in >1) 4673 10159 581503484 2 124439 174940
ps5 (decontam) 4662 10147 579318310 2 124264 174962
ps6 (no duplicates) 4136 10071 538600483 2 130223 183923
ps7 (samples with ≥25k) 3837 10061 536557613 25070 139838 187562
ps8 (rarefied to 25k) 3837 10061 95925000 25000 25000 0
nsamples ntaxa total_count min av sd
ps1 (infant stool) 1856 10568 269774889 4 145353 142163
ps1 (maternal stool) 466 21698 62211349 78 133501 107906
ps1 (breastmilk) 1334 50579 146574829 13 109876 147375
Mean retention % after taxon filtering (ps5):
* Infant stools = 99.9
* Maternal stools = 96.8
* Breastmilk = 93.5
nsamples ntaxa total_count min av sd
ps7 (infant stool) 1698 4662 250856755 25070 147737 145600
ps7 (maternal stool) 440 4423 57597054 31309 130902 105042
ps7 (breastmilk) 1206 7386 131038347 25088 108655 141520
nsamples ntaxa total_count min av sd
ps7 (all stool) 2138 6415 308453809 25070 144272 138374
nsamples ntaxa total_count min_count av_count NA
ps8 (infant stool) 1698 4462 42450000 25000 25000 0
ps8 (maternal stool) 440 4366 11000000 25000 25000 0
ps8 (breastmilk) 1206 7360 30150000 25000 25000 0
Ten most frequent taxanomic assignments displayed for each group. Remaining taxa grouped as ‘other’. Bar heights represent proportion of RSVs assigned to taxon, independent of their relative abundance.
BSctrl MCctrl MSctrl
31 33 21
country sample_type R2_w p_w R2_u p_u n_runs n_samples
1 IND week of life 1 0.028 0.037 0.034 0.001 7 289
2 IND week of life 4 0.022 0.328 0.037 0.001 7 287
3 IND week of life 6 0.027 0.103 0.032 0.001 7 289
4 IND week of life 10 0.022 0.365 0.033 0.001 7 282
5 IND mother 0.034 0.001 0.033 0.001 7 288
6 UK week of life 1 0.051 0.121 0.062 0.008 4 71
8 UK week of life 6 0.068 0.031 0.085 0.001 4 58
9 UK week of life 10 0.068 0.053 0.068 0.035 4 57
15 MLW mother 0.042 0.016 0.038 0.160 4 87
country sample_type R2_w p_w R2_u p_u n_runs n_samples
1 IND week of life 1 0.017 0.005 0.021 0.001 4 270
2 IND week of life 7 0.024 0.001 0.026 0.001 4 259
3 IND week of life 11 0.027 0.001 0.032 0.001 4 260
7 MLW week of life 1 0.025 0.112 0.030 0.003 3 100
8 MLW week of life 7 0.034 0.016 0.043 0.001 3 90
9 MLW week of life 11 0.035 0.018 0.038 0.001 3 85
India Malawi UK
BS1 30 19 29
BS5 28 22 30
MS1 30 29 26
See outputs of analysis module 1 for further details of feature table filtering process.
Number of taxa present at ≥0.1% abundance in ≥1% of samples: 252
Number of samples include: 2086
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India 305 305 305 301 301 301 304 298
India_e 166 166 166 163 163 163 165 162
India_u 138 138 138 137 136 136 138 134
Malawi 103 103 103 78 83 83 87 63
UK 56 54 49 30 48 47 0 51
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India 298 288 289 287 289 282 307
India_e 162 156 155 156 154 160 166
India_u 134 129 131 128 132 120 138
Malawi 63 83 81 75 68 61 119
UK 51 57 59 59 53 55 60
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India_r 85 85 85 83 83 83 84 83
India_nr 220 220 220 218 217 217 220 214
India_r_e 51 51 51 50 50 50 50 50
India_nr_e 115 115 115 113 113 113 115 112
India_r_u 34 34 34 33 33 33 34 33
India_nr_u 104 104 104 104 103 103 104 101
Malawi_r 24 24 24 16 16 16 19 12
Malawi_nr 79 79 79 62 62 62 68 41
UK_r 27 27 23 13 23 22 0 24
UK_nr 24 24 19 14 20 20 0 22
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India_r 83 77 79 76 79 79 85
India_nr 214 209 208 209 208 202 220
India_r_e 50 46 47 46 46 49 51
India_nr_e 112 110 108 110 108 111 115
India_r_u 33 31 32 30 33 30 34
India_nr_u 101 98 99 98 99 90 104
Malawi_r 12 16 18 15 12 9 24
Malawi_nr 41 58 55 56 54 44 79
UK_r 24 25 27 26 25 25 27
UK_nr 20 23 23 24 23 24 24
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India_r 81 81 81 81 80 80 81 81
India_nr 222 222 222 218 219 219 221 215
India_r_e 29 29 29 29 28 28 29 29
India_nr_e 135 135 135 132 133 133 134 131
India_r_u 52 52 52 52 51 51 52 51
India_nr_u 86 86 86 85 85 85 86 83
Malawi_r 45 45 45 36 34 34 41 32
Malawi_nr 40 40 40 28 37 37 34 25
UK_r 52 49 46 26 44 44 0 48
UK_nr 4 5 3 4 4 3 0 3
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India_r 81 73 73 77 76 74 82
India_nr 215 213 214 208 211 206 223
India_r_e 29 26 26 28 26 26 29
India_nr_e 131 128 127 126 126 132 135
India_r_u 51 46 46 48 49 47 52
India_nr_u 83 83 85 80 83 73 86
Malawi_r 32 42 39 32 25 33 56
Malawi_nr 25 27 29 32 32 21 45
UK_r 48 53 55 54 49 51 55
UK_nr 3 4 4 5 4 4 5
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India_r 150 150 150 149 147 147 150 147
India_nr 152 152 152 149 151 151 151 148
India_r_e 65 65 65 65 63 63 65 62
India_nr_e 99 99 99 96 98 98 98 98
India_r_u 84 84 84 83 82 82 84 83
India_nr_u 53 53 53 53 53 53 53 50
Malawi_r 41 41 41 29 35 35 36 28
Malawi_nr 20 20 20 13 19 19 19 16
UK_r 50 49 46 26 44 44 0 48
UK_nr 2 2 0 1 2 1 0 1
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India_r 147 140 139 142 142 135 151
India_nr 148 145 147 142 144 144 153
India_r_e 62 61 60 62 60 61 65
India_nr_e 98 93 93 92 92 97 99
India_r_u 83 77 77 78 80 72 84
India_nr_u 50 51 53 49 51 47 53
Malawi_r 28 34 31 30 27 30 50
Malawi_nr 16 14 16 15 16 12 22
UK_r 48 53 53 54 47 51 54
UK_nr 1 1 2 2 2 2 2
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India_r 181 181 181 179 176 176 180 175
India_nr 121 121 121 119 121 121 121 119
India_r_e 87 87 87 86 84 84 86 83
India_nr_e 77 77 77 75 77 77 77 77
India_r_u 93 93 93 92 91 91 93 91
India_nr_u 44 44 44 44 44 44 44 42
Malawi_r 43 43 43 29 33 33 38 25
Malawi_nr 18 18 18 13 17 17 17 12
UK_r 46 46 40 23 40 40 0 43
UK_nr 2 2 0 1 2 1 0 1
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India_r 175 167 168 167 169 164 181
India_nr 119 116 116 115 115 114 121
India_r_e 83 81 81 82 79 83 87
India_nr_e 77 73 72 72 73 75 77
India_r_u 91 85 86 84 89 80 93
India_nr_u 42 43 44 43 42 39 44
Malawi_r 25 30 27 29 27 25 43
Malawi_nr 12 12 14 13 15 11 18
UK_r 41 45 45 46 43 45 46
UK_nr 1 1 2 2 2 2 2
BB1_IgA BB2_IgA MB1_IgA BM1_IgA BS3_A1AT BS3_MPO BB1_A1AG BS5_A1AT
India 305 305 305 301 300 300 304 297
India_e 166 166 166 163 163 163 165 162
India_u 138 138 138 137 136 136 138 134
Malawi 103 103 103 78 78 78 87 53
UK 51 54 45 29 43 42 0 48
BS5_MPO MS1 BS1 BS2 BS3 BS5 n
India 297 286 287 285 287 281 305
India_e 162 156 155 156 154 160 166
India_u 134 129 131 128 132 120 138
Malawi 53 74 73 71 66 53 103
UK 46 51 53 53 48 51 54
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] FSA_0.9.0 ALDEx2_1.18.0
[3] sjstats_0.18.0 ggExtra_0.9
[5] formattable_0.2.0.1 NBZIMM_1.0
[7] inlmisc_0.5.2 decontam_1.6.0
[9] ggtree_2.0.4 wesanderson_0.3.6
[11] phangorn_2.5.5 ape_5.4-1
[13] DECIPHER_2.14.0 RSQLite_2.2.1
[15] Biostrings_2.54.0 XVector_0.26.0
[17] cowplot_1.1.0 scales_1.1.1
[19] RVAideMemoire_0.9-78 DescTools_0.99.38
[21] ggsignif_0.6.0 binom_1.1-1
[23] shiny_1.5.0 randomcoloR_1.1.0.1
[25] DESeq2_1.26.0 SummarizedExperiment_1.16.1
[27] DelayedArray_0.12.3 BiocParallel_1.20.1
[29] Biobase_2.46.0 GenomicRanges_1.38.0
[31] GenomeInfoDb_1.22.1 IRanges_2.20.2
[33] S4Vectors_0.24.4 BiocGenerics_0.32.0
[35] crossval_1.0.3 UpSetR_1.4.0
[37] labdsv_2.0-1 mgcv_1.8-33
[39] nlme_3.1-149 ggpubr_0.4.0
[41] data.table_1.12.8 corrplot_0.84
[43] ZIBR_0.1 vegan_2.5-6
[45] lattice_0.20-41 permute_0.9-5
[47] randomForest_4.6-14 matrixStats_0.57.0
[49] lme4_1.1-23 Matrix_1.2-18
[51] reshape2_1.4.4 pheatmap_1.0.12
[53] DT_0.16 plotly_4.9.3
[55] cluster_2.1.0 tidyr_1.1.2
[57] dplyr_1.0.2 magrittr_1.5
[59] plyr_1.8.6 kableExtra_1.2.1
[61] gridExtra_2.3 RColorBrewer_1.1-2
[63] knitr_1.30 ggplot2_3.3.2
[65] phyloseq_1.30.0
loaded via a namespace (and not attached):
[1] estimability_1.3 coda_0.19-4 bit64_4.0.5
[4] rpart_4.1-15 RCurl_1.98-1.2 generics_0.0.2
[7] bit_4.0.4 webshot_0.5.2 xml2_1.3.2
[10] httpuv_1.5.4 xfun_0.18 hms_0.5.3
[13] evaluate_0.14 promises_1.1.1 readxl_1.3.1
[16] igraph_1.2.6 DBI_1.1.0 geneplotter_1.64.0
[19] htmlwidgets_1.5.3 purrr_0.3.4 ellipsis_0.3.1
[22] backports_1.1.10 V8_3.2.0 insight_0.9.6
[25] annotate_1.64.0 vctrs_0.3.4 sjlabelled_1.1.7
[28] abind_1.4-5 withr_2.3.0 checkmate_2.0.0
[31] rgdal_1.5-18 emmeans_1.5.1 treeio_1.10.0
[34] lazyeval_0.2.2 crayon_1.3.4 flexdashboard_0.5.2
[37] genefilter_1.68.0 labeling_0.3 pkgconfig_2.0.3
[40] nnet_7.3-14 rlang_0.4.8 lifecycle_0.2.0
[43] miniUI_0.1.1.1 modelr_0.1.8 cellranger_1.1.0
[46] raster_3.3-13 carData_3.0-4 Rhdf5lib_1.8.0
[49] boot_1.3-25 base64enc_0.1-3 png_0.1-7
[52] viridisLite_0.3.0 parameters_0.8.6 rootSolve_1.8.2.1
[55] bitops_1.0-6 blob_1.2.1 stringr_1.4.0
[58] jpeg_0.1-8.1 rstatix_0.6.0 memoise_1.1.0
[61] zlibbioc_1.32.0 compiler_3.6.1 ade4_1.7-15
[64] htmlTable_2.1.0 Formula_1.2-4 MASS_7.3-53
[67] tidyselect_1.1.0 stringi_1.5.3 forcats_0.5.0
[70] yaml_2.2.1 locfit_1.5-9.4 latticeExtra_0.6-29
[73] grid_3.6.1 fastmatch_1.1-0 tools_3.6.1
[76] lmom_2.8 rio_0.5.16 rstudioapi_0.11
[79] foreach_1.5.1 foreign_0.8-71 gld_2.6.2
[82] farver_2.0.3 Rtsne_0.15 digest_0.6.25
[85] rvcheck_0.1.8 BiocManager_1.30.10 quadprog_1.5-8
[88] Rcpp_1.0.5 car_3.0-10 broom_0.7.1
[91] performance_0.5.0 later_1.1.0.1 httr_1.4.2
[94] AnnotationDbi_1.48.0 effectsize_0.3.3 colorspace_1.4-1
[97] rvest_0.3.6 XML_3.99-0.3 splines_3.6.1
[100] statmod_1.4.34 tidytree_0.3.3 expm_0.999-5
[103] sp_1.4-4 multtest_2.42.0 Exact_2.1
[106] xtable_1.8-4 jsonlite_1.7.1 nloptr_1.2.2.2
[109] R6_2.4.1 Hmisc_4.4-1 pillar_1.4.6
[112] htmltools_0.5.0 mime_0.9 glue_1.4.2
[115] fastmap_1.0.1 minqa_1.2.4 class_7.3-17
[118] codetools_0.2-17 mvtnorm_1.1-1 tibble_3.0.4
[121] curl_4.3 zip_2.1.1 openxlsx_4.2.2
[124] survival_3.2-7 rmarkdown_2.4 biomformat_1.14.0
[127] munsell_0.5.0 e1071_1.7-4 rhdf5_2.30.1
[130] GenomeInfoDbData_1.2.2 iterators_1.0.13 sjmisc_2.8.5
[133] haven_2.3.1 gtable_0.3.0 bayestestR_0.7.2
.